btw, you should not need to run mri_annotation2label twice. On 11/21/2013 10:44 AM, Mojdeh Zamyadi wrote:
Hi all,
I want to convert the cortical labels I get in freeSurfer to volumetric ROIs in the subject space and I've followed the steps mentioned in: http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-fr...
except since I'm interested in lobe mapping I've changed the first commands, more specifically these are the different command I've run:
- mri_annotation2label --subject P2 --hemi lh --outdir
freeSurfer_Results/P2/labels/ --lobesStrict freeSurfer_Results/P2/labels/freeSurfer_lobes
- mri_annotation2label --hemi lh --subject P2 --outdir
freeSurfer_Results/P2/labels/ --annotation freeSurfer_Results/P2/labels/lh.freeSurfer_lobes.annot
- tkregister2 --mov freeSurfer_Results/P2/mri/rawavg.mgz --noedit --s
P2 --regheader --reg freeSurfer_Results/P2/register.dat
- mri_label2vol --label freeSurfer_Results/P2/labels/lh.parietal.label
--temp freeSurfer_Results/P2/mri/rawavg.mgz --subject P2 --hemi lh --o freeSurfer_Results/P2/labels/lh.parietal.nii.gz --proj frac 0 1 .1 --fillthresh 1 --reg freeSurfer_Results/P2/register.dat
the issue I have now is that the final ROI I get (e.g. "lh.parietal.nii.gz") looks like a series of disconnected points! I was wondering how I can get a smooth (i.e. filled) volumetric ROI?
Thanks, -Mojdeh
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